Quantum chemical package Jaguar: A survey of recent developments and unique features.

This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach.

Large Computational Survey of Intrinsic Reactivity of Aromatic Carbon Atoms with Respect to a Model Aldehyde Oxidase.

Aldehyde oxidase (AOX) and other related molybdenum-containing enzymes are known to oxidize the C-H bonds of aromatic rings. This process contributes to the metabolism of pharmaceutical compounds and, therefore, is of vital importance to drug pharmacokinetics. The present work describes an automated computational workflow and its use for the prediction of intrinsic reactivity of small aromatic molecules toward a minimal model of the active site of AOX.

Accurate Quantum Chemical Reaction Energies for Lithium-Mediated Electrolyte Decomposition and Evaluation of Density Functional Approximations.

An important concern related to the performance of Li-ion batteries is the formation of a solid electrolyte interphase on the surface of the anode. This film is formed from the decomposition of electrolytes and can have important effects on the stability and performance. Here, we evaluate the decomposition pathway of ethylene carbonate and related organic electrolyte molecules using a series of density functional approximations and correlated wave function (WF) methods, including the coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and auxiliary-field quantum Monte Carlo (AFQMC).

Development of scalable and generalizable machine learned force field for polymers.

Understanding and predicting the properties of polymers is vital to developing tailored polymer molecules for desired applications. Classical force fields may fail to capture key properties, for example, the transport properties of certain polymer systems such as polyethylene glycol. As a solution, we present an alternative potential energy surface, a charge recursive neural network (QRNN) model trained on DFT calculations made on smaller atomic clusters that generalizes well to oligomers comprising larger atomic clusters or longer chains.

High-Dimensional Neural Network Potential for Liquid Electrolyte Simulations.

Liquid electrolytes are one of the most important components of Li-ion batteries, which are a critical technology of the modern world. However, we still lack the computational tools required to accurately calculate key properties of these materials (viscosity and ionic diffusivity) from first principles necessary to support improved designs. In this work, we report a machine learning-based force field for liquid electrolyte simulations, which bridges the gap between the accuracy of range-separated hybrid density functional theory and the efficiency of classical force fields.

Transferable Neural Network Potential Energy Surfaces for Closed-Shell Organic Molecules: Extension to Ions.

Transferable high dimensional neural network potentials (HDNNPs) have shown great promise as an avenue to increase the accuracy and domain of applicability of existing atomistic force fields for organic systems relevant to life science. We have previously reported such a potential (Schrödinger-ANI) that has broad coverage of druglike molecules. We extend that work here to cover ionic and zwitterionic druglike molecules expected to be relevant to drug discovery research activities.

Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package.

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods.

Pattern-free generation and quantum mechanical scoring of ring-chain tautomers.

In contrast to the computational generation of conventional tautomers, the analogous operation that would produce ring-chain tautomers is rarely available in cheminformatics codes. This is partly due to the perceived unimportance of ring-chain tautomerism and partly because specialized algorithms are required to realize the non-local proton transfers that occur during ring-chain rearrangement. Nevertheless, for some types of organic compounds, including sugars, warfarin analogs, fluorescein dyes and some drug-like compounds, ring-chain tautomerism cannot be ignored.

Toward Atomistic Modeling of Irreversible Covalent Inhibitor Binding Kinetics.

Covalent inhibitors have emerged as an important drug class in recent years, largely due to their many unique advantages as compared to noncovalent inhibitors, including longer duration of action, lower prolonged systemic exposure, higher potency, and selectivity. However, the potential off-target toxicity of covalent inhibitors, particularly of irreversible covalent inhibitors, represents a great challenge in covalent drug development. Therefore, accurate calculation of protein covalent inhibitor reaction kinetics to guide the design of selective inhibitors would greatly benefit covalent drug discovery efforts.

Automated Transition State Search and Its Application to Diverse Types of Organic Reactions.

Transition state search is at the center of multiple types of computational chemical predictions related to mechanistic investigations, reactivity and regioselectivity predictions, and catalyst design. The process of finding transition states in practice is, however, a laborious multistep operation that requires significant user involvement. Here, we report a highly automated workflow designed to locate transition states for a given elementary reaction with minimal setup overhead.

Rapid computation of intermolecular interactions in molecular and ionic clusters: self-consistent polarization plus symmetry-adapted perturbation theory.

A method that we have recently introduced for rapid computation of intermolecular interaction energies is reformulated and subjected to further tests. The method employs monomer-based self-consistent field calculations with an electrostatic embedding designed to capture many-body polarization (the "XPol" procedure), augmented by pairwise symmetry-adapted perturbation theory (SAPT) to capture dispersion and exchange interactions along with any remaining induction effects. A rigorous derivation of the XPol+SAPT methodology is presented here, which demonstrates that the method is systematically improvable, and moreover introduces some additional intermolecular interactions as compared to the more heuristic derivation that was presented previously.

Structure of the aqueous electron: assessment of one-electron pseudopotential models in comparison to experimental data and time-dependent density functional theory.

The prevailing structural paradigm for the aqueous electron is that of an s-like ground-state wave function that inhabits a quasi-spherical solvent cavity, a viewpoint that is supported by numerous atomistic simulations using various one-electron pseudopotential models. This conceptual picture has recently been challenged, however, on the basis of results obtained from a new electron-water pseudopotential model that predicts a more delocalized wave function and no well-defined solvent cavity. Here, we examine this new model in comparison to two alternative, cavity-forming pseudopotential models.

Theoretical characterization of four distinct isomer types in hydrated-electron clusters, and proposed assignments for photoelectron spectra of water cluster anions.

Water cluster anions, (H(2)O)(N)(-), are examined using mixed quantum/classical molecular dynamics based on a one-electron pseudopotential model that incorporates many-body polarization and predicts vertical electron detachment energies (VDEs) with an accuracy of ~0.1 eV. By varying the initial conditions under which the clusters are formed, we are able to identify four distinct isomer types that exhibit different size-dependent VDEs.

A Simple Algorithm for Determining Orthogonal, Self-Consistent Excited-State Wave Functions for a State-Specific Hamiltonian: Application to the Optical Spectrum of the Aqueous Electron.

We recently introduced a mixed quantum/classical model for the hydrated electron that includes electron/water polarization in a self-consistent fashion, using a polarizable force field for the water molecules [ J. Chem. Phys.

Comment on "Does the hydrated electron occupy a cavity?".

Larsen et al. (Reports, 2 July 2010, p. 65) suggest that, contrary to the established paradigm, the aqueous electron does not carve out and occupy a cavity in liquid water.

An efficient, fragment-based electronic structure method for molecular systems: self-consistent polarization with perturbative two-body exchange and dispersion.

We report a fragment-based electronic structure method, intended for the study of clusters and molecular liquids, that incorporates electronic polarization (induction) in a self-consistent fashion but treats intermolecular exchange and dispersion interactions perturbatively, as post-self-consistent field corrections, using a form of pairwise symmetry-adapted perturbation theory. The computational cost of the method scales quadratically as a function of the number of fragments (monomers), but could be made to scale linearly by exploiting distance-dependent thresholds. Extensive benchmark calculations are reported using the S22 database of high-level ab initio binding energies for dimers, and we find that average errors can be reduced to <1 kcal/mol with a suitable choice of basis set.

A one-electron model for the aqueous electron that includes many-body electron-water polarization: Bulk equilibrium structure, vertical electron binding energy, and optical absorption spectrum.

Previously, we reported an electron-water pseudopotential designed to be used in conjunction with a polarizable water model, in order to describe the hydrated electron [L. D. Jacobson et al.

Polarization-bound quasi-continuum states are responsible for the "blue tail" in the optical absorption spectrum of the aqueous electron.

The electronic absorption spectrum of the aqueous electron in bulk water has been simulated using long-range-corrected time-dependent density functional theory as well as mixed quantum/classical molecular dynamics based on a one-electron model in which electron-water polarization is treated self-consistently. Both methodologies suggest that the high-energy Lorentzian tail that is observed experimentally arises mostly from delocalized bound-state excitations of the electron rather than bound-to-continuum excitations, as is usually assumed. Excited states in the blue tail are bound only by polarization of the solvent electron density.

The static-exchange electron-water pseudopotential, in conjunction with a polarizable water model: a new Hamiltonian for hydrated-electron simulations.

Previously, Turi and Borgis [J. Chem. Phys.